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Computer modeling is now an integral part of research in evolutionary biology. The advent of increased processing power in the personal computer, coupled with the availability of languages such as R, SPLUS, Mathematica, Maple, Mathcad, and MATLAB, has ensured that the development and analysis of computer models of evolution is now within the capabilities of most graduate students. However, there are two hurdles that tend to discourage students from making full use of the power of computer modeling. The first is the general problem of formulating the question and the second is its implementation using an appropriate computer language.Modelling Evolution outlines how evolutionary questions are formulated and how, in practice, they can be resolved by analytical and numerical methods (with the emphasis being on the latter). Following a general introduction to computer modeling, successive chapters describe "Fisherian" optimality models, invasibility analysis, genetic models, game theoretic models, and dynamic programming. A common chapter plan facilitates tuition and comprises an introduction (in which the general approach and methods are described) followed by a series of carefully structured scenarios that have been selected to highlight particular aspects of evolutionary modeling. Coding for each example is provided in either R or MATLAB since both of these programs are readily available and extensively used. This coding is available on the author's web site allowing easy implementation and study of the programs. Each chapter concludes with a list of exemplary papers which have been chosen on the basis of how well they explain and illustrate the techniques discussed in the chapter.
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Modeling Evolution
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Modeling Evolution an introduction to numerical methods D. A. Roff
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Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York # D. A. Roff 2010 The moral rights of the author have been asserted Database right Oxford University Press (maker) First published 2010 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Data available Typeset by SPI Publisher Services, Pondicherry, India Printed in Great Britain on acid-free paper by CPI Antony Rowe Chippenham, Wiltshire ISBN 978–0–19–957114–7 1 3 5 7 9 10 8 6 4 2
Contents 1 Overview
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1.1 Introduction 1 1.1.1 The aim of this book 1 1.1.2 Why R and MATLAB? 2 1.2 Operational definitions of fitness 3 1.2.1 Constant environment, density‐independent, stable‐age dis